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* gnu: r-survival: Update to 2.43-3.Ricardo Wurmus2019-01-12
| | | | * gnu/packages/statistics.scm (r-survival): Update to 2.43-3.
* gnu: r-argparse: Update to 2.0.0.Ricardo Wurmus2019-01-12
| | | | | * gnu/packages/cran.scm (r-argparse): Update to 2.0.0. [propagated-inputs]: Add r-r6; remove r-proto.
* gnu: r-callr: Update to 3.1.1.Ricardo Wurmus2019-01-12
| | | | | * gnu/packages/cran.scm (r-callr): Update to 3.1.1. [propagated-inputs]: Remove r-base64enc.
* gnu: r-readxl: Update to 1.2.0.Ricardo Wurmus2019-01-12
| | | | | * gnu/packages/cran.scm (r-readxl): Update to 1.2.0. [propagated-inputs]: Add r-progress.
* gnu: r-pracma: Update to 2.2.2.Ricardo Wurmus2019-01-12
| | | | * gnu/packages/maths.scm (r-pracma): Update to 2.2.2.
* gnu: r-rcpparmadillo: Update to 0.9.200.5.0.Ricardo Wurmus2019-01-12
| | | | * gnu/packages/statistics.scm (r-rcpparmadillo): Update to 0.9.200.5.0.
* gnu: r-processx: Update to 3.2.1.Ricardo Wurmus2019-01-12
| | | | | * gnu/packages/cran.scm (r-processx): Update to 3.2.1. [propagated-inputs]: Remove r-assertthat, r-crayon, and r-testthat.
* gnu: r-sjlabelled: Update to 1.0.16.Ricardo Wurmus2019-01-12
| | | | | * gnu/packages/cran.scm (r-sjlabelled): Update to 1.0.16. [propagated-inputs]: Remove r-tibble and r-tidyselect.
* gnu: r-broom: Update to 0.5.1.Ricardo Wurmus2019-01-12
| | | | | * gnu/packages/cran.scm (r-broom): Update to 0.5.1. [propagated-inputs]: Add r-generics.
* gnu: Add r-generics.Ricardo Wurmus2019-01-12
| | | | * gnu/packages/cran.scm (r-generics): New variable.
* gnu: r-curl: Update to 3.3.Ricardo Wurmus2019-01-12
| | | | | | * gnu/packages/cran.scm (r-curl): Update to 3.3. [inputs]: Add zlib. [native-inputs]: Add pkg-config.
* gnu: r-readr: Update to 1.3.1.Ricardo Wurmus2019-01-12
| | | | | * gnu/packages/statistics.scm (r-readr): Update to 1.3.1. [propagated-inputs]: Add r-clipr and r-crayon.
* gnu: r-mvabund: Update to 4.0.1.Ricardo Wurmus2019-01-12
| | | | * gnu/packages/cran.scm (r-mvabund): Update to 4.0.1.
* gnu: r-writexl: Update to 1.1.Ricardo Wurmus2019-01-12
| | | | * gnu/packages/cran.scm (r-writexl): Update to 1.1.
* gnu: r-jsonlite: Update to 1.6.Ricardo Wurmus2019-01-12
| | | | * gnu/packages/cran.scm (r-jsonlite): Update to 1.6.
* import: cran: Suggest input changes.Ricardo Wurmus2019-01-12
| | | | | * guix/import/cran.scm (latest-cran-release, latest-bioconductor-release): Return input-changes.
* refresh: Suggest input changes when updating.Ricardo Wurmus2019-01-12
| | | | | | | | | | * guix/upstream.scm (<upstream-source>)[input-changes]: New field. (<upstream-input-change>): New record. (upstream-input-change?, upstream-input-change-name, upstream-input-change-type, upstream-input-change-action, changed-inputs): New procedures. (package-update): Pass along input changes. * guix/script/refresh.scm (update-package): Process input changes.
* gnu: python-pillow: Update homepage.Kei Kebreau2019-01-12
| | | | * gnu/packages/python.scm (python-pillow)[homepage]: Update URL.
* gnu: python-pillow: Update to 5.4.0Kei Kebreau2019-01-12
| | | | | * gnu/packages/python.scm (python-pillow): Update to 5.4.0. [arguments]: Add 'patch-ldconfig' phase.
* gnu: Sort package modules in (gnu packages guile).Ricardo Wurmus2019-01-12
| | | | * gnu/packages/guile.scm: Sort list of gnu/packages modules.
* gnu: impressive: Update to 0.12.0.Ricardo Wurmus2019-01-12
| | | | * gnu/packages/pdf.scm (impressive): Update to 0.12.0.
* gnu: Move Java compression packages to new module.Ricardo Wurmus2019-01-12
| | | | | | | | | | * gnu/packages/compression.scm (bitshuffle-for-snappy): Export variable. (java-snappy, java-snappy-1, java-iq80-snappy, java-jbzip2, java-tukaani-xz): Move these variables from here... * gnu/packages/java-compression.scm: ...to this new file. * gnu/local.mk (GNU_SYSTEM_MODULES): Add it. * gnu/packages/java.scm, gnu/packages/bioinformatics.scm: Adjust module references.
* gnu: Add Bochs.guy fleury iteriteka2019-01-11
| | | | | | * gnu/packages/virtualization.scm (bochs): New variable. Signed-off-by: Leo Famulari <leo@famulari.name>
* gnu: Stellarium: Update to 0.18.3.Leo Famulari2019-01-11
| | | | | * gnu/packages/astronomy.scm (stellarium): Update to 0.18.3. [arguments]: Skip a broken test.
* gnu: opendht: Make argon2 a propagated input so that its .pc is found.Pierre Neidhardt2019-01-11
| | | | | * gnu/packages/networking.scm (opendht)[inputs]: Remove argon2. [propagated-inputs]: Add it here.
* gnu: opendht: Use jsoncpp and restbed.Pierre Neidhardt2019-01-11
| | | | | * gnu/packages/crypto.scm (opendht): Move definition to networking.scm. * gnu/packages/networking.scm (opendht)[inputs]: Add jsoncpp and restbed.
* gnu: Add restbed.Pierre Neidhardt2019-01-11
| | | | * gnu/packages/networking.scm (restbed): New variable.
* gnu: libupnp: Update to 1.6.25.Pierre Neidhardt2019-01-11
| | | | * gnu/packages/upnp.scm (libupnp): Update to 1.6.25.
* gnu: kinit: Use KDEINIT5_LIBRARY_PATH to search for dynlibs.Hartmut Goebel2019-01-11
| | | | | | | | | | | Using LIBRARY_PATH was introduced in 16b8aff85bcdb9799496c4a27257210cd45158e5, but is wrong since this variable is used by the compiler (gcc) at link time. * gnu/packages/patches/kinit-kdeinit-libpath.patch: Change LIBRARY_PATH to KDEINIT5_LIBRARY_PATH. * gnu/packages/kde-frameworks.scm (kinit)[native-search-paths]: New field.
* Revert "gnu: emacs-ghub: Update to 3.2.0."Jelle Licht2019-01-11
| | | | | | This change should be applied once we update our magit package. This reverts commit b96f0e6ff9f8f36d250b5ae94a908272babb35cf.
* guix build: Re-purpose '--verbosity' and add '--debug'.Ludovic Courtès2019-01-11
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | The previous '--verbosity' option was misleading and rarely what users were looking for. The new option provides a consistent way to choose whether or not to display the build log. * guix/scripts/build.scm (show-build-options-help): Remove "--verbosity" and add "--debug". (set-build-options-from-command-line): Use the 'debug key of OPTS for #:verbosity. (%standard-build-options): Change "verbosity" to "debug". Use 'string->number*' instead of 'string->number'. (%default-options): Change 'verbosity to 'debug and add a 'verbosity key. (show-help): Add '--verbosity'. (%options): Likewise, and change '--quiet' to set the 'verbosity key of RESULT. (guix-build): Use 'with-status-verbosity' instead of parameterizing CURRENT-BUILD-OUTPUT-PORT, honor the 'verbosity key of OPTS, and remove 'quiet?'. * guix/scripts/environment.scm (show-help, %options): Add '--verbosity'. (%default-options): Add 'debug'. (guix-environment): Honor the 'verbosity key of OPTS. * guix/scripts/pack.scm (%default-options): Add 'debug. (%options, show-help): Add '--verbosity'. (guix-pack): Honor the 'verbosity key of OPTS. * guix/scripts/package.scm (%default-options): Add 'debug. (show-help, %options): Add '--verbosity'. Mark '--verbose' as deprecated and change it to set 'verbosity. (guix-package): Honor the 'verbosity key of OPTS and remove 'verbose?'. * guix/scripts/pull.scm (%default-options): Add 'debug. (show-help, %options): Add '--verbosity'. (guix-pull): Honor the 'verbosity key of OPTS. * guix/scripts/system.scm (show-help, %options): Add '--verbosity'. (%default-options): Add 'debug. (guix-system): Honor the 'verbosity key of OPTS. * guix/scripts/archive.scm (%default-options): Add 'debug, 'print-build-trace?, 'print-extended-build-trace?, and 'multiplexed-build-output?. (show-help, %options): Add '--verbosity'. (export-from-store): Remove call to 'set-build-options-from-command-line'. (guix-archive): Wrap body in 'with-status-verbosity'. Add call to 'set-build-options-from-command-line. * doc/guix.texi (Common Build Options): Document '--verbosity' and '--debug'. (Additional Build Options): Adjust description of '--quiet'.
* status: Add 'with-status-verbosity'.Ludovic Courtès2019-01-11
| | | | | | | | | | | | | * guix/status.scm (logger-for-level, call-with-status-verbosity): New procedures. (with-status-verbosity): New macro. * guix/scripts/environment.scm (guix-environment): Use 'with-status-verbosity' instead of 'with-status-report'. * guix/scripts/pack.scm (guix-pack): Likewise. * guix/scripts/package.scm (guix-package): Likewise. * guix/scripts/pull.scm (guix-pull): Likewise. * guix/scripts/system.scm (guix-system): Likewise. * build-aux/run-system-tests.scm (run-system-tests): Likewise.
* refresh: Turn on warnings when '--manifest' is used.Ludovic Courtès2019-01-11
| | | | * guix/scripts/refresh.scm (guix-refresh): Set WARN? when '-m' is used.
* refresh: Refactor option handling and '--recursive'.Ludovic Courtès2019-01-11
| | | | | | | | | | | | | | This allows us to combine '--recursive' with other options (-u, -m, etc.), turns off warnings when '--recursive' is used, and avoids the hazards of I/O in the presence of multithreading. * guix/scripts/refresh.scm (options->packages): New procedure, with code formerly in 'guix-refresh'. (refresh-recursive): Remove. (guix-refresh)[keep-newest, core-package?, args-packages, packages]: Remove. [warn?]: Set to #f when RECURSIVE? is true. Call 'options->packages' in monadic context.
* gnu: Add emacs-general.Gabriel Hondet2019-01-11
| | | | | | | [[PGP Signed Part:Good signature from 31BC8105F659D425 Gabriel Hondet <gabrielhondet@gmail.com> (trust undefined) created at 2019-01-06T10:42:43+0100 using RSA]] * gnu/packages/emacs.scm (emacs-general): New variable. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
* services: Deprecate a few more service procedures.Ludovic Courtès2019-01-11
| | | | | | | | | | | | | | | | | | These procedures were already either undocumented (and de facto deprecated) or documented as deprecated or redundant. * gnu/services/base.scm (guix-service, guix-publish-service): Mark as deprecated. * gnu/services/mcron.scm (mcron-service): Likewise. * gnu/services/networking.scm (tor-service): Likewise. * doc/guix.texi (Scheduled Job Execution): Remove 'mcron-service' and adjust example. (Networking Services): Remove 'tor-service'. * gnu/tests/base.scm (%mcron-os): Use 'mcron-service-type' instead of 'mcron-service'. * gnu/tests/networking.scm (%tor-os): Use 'tor-service-type' instead of 'tor-service'. * tests/guix-system.sh: Likewise.
* tests: Nitpick on Docker test.Ludovic Courtès2019-01-11
| | | | | | | This is a followup to 7d8a4eeacc534c8742e0b22d855aa73e5ab66b7f. * gnu/local.mk (GNU_SYSTEM_MODULES): Add gnu/tests/docker.scm. * gnu/tests/docker.scm: Update copyright line.
* gnu: wine-staging: Hard-code vulkan loader.Rutger Helling2019-01-11
| | | | | | | * gnu/packages/wine.scm (wine-staging-patchset-data): Fix indentation. * gnu/packages/wine.scm (wine-staging)[arguments]: Add 'wrap-executable phase. * gnu/packages/wine.scm (wine64-staging)[arguments]: Add 'wrap-executable phase. Copy the real wine-preloader instead of the wrapped version.
* gnu: jamm: Remove broken "build" phase.Ricardo Wurmus2019-01-11
| | | | * gnu/packages/bioinformatics.scm (jamm)[arguments]: Remove "build" phase.
* services: docker: Update comment.Danny Milosavljevic2019-01-11
| | | | * gnu/services/docker.scm (docker-shepherd-service): Update comment.
* gnu: gexiv2: Update to 0.10.10.Leo Famulari2019-01-10
| | | | * gnu/packages/gnome.scm (gexiv2): Update to 0.10.10.
* build-system: texlive: Do not hide build output.Ricardo Wurmus2019-01-10
| | | | | * guix/build/texlive-build-system.scm (compile-with-latex): Use "nonstopmode" instead of "batchmode".
* build-system: texlive: Do not truncate lines.Ricardo Wurmus2019-01-10
| | | | | * guix/build/texlive-build-system.scm (configure): Set environment variables to prevent build output lines from being truncated.
* gnu: Update texlive packages.Ricardo Wurmus2019-01-10
| | | | | | | | | | | | | | | | | | | | | | | | | | | | * guix/build-system/texlive.scm (%texlive-tag, %texlive-revision): Update to texlive-2018.2, revision 49435. * gnu/packages/tex.scm (texlive-dvips, texlive-generic-unicode-data, texlive-generic-dehyph-exptl, texlive-generic-hyph-utf8, texlive-fontname, texlive-fonts-cm, texlive-tex-plain, texlive-latex-base, texlive-latex-graphics, texlive-latex-graphics, texlive-latex-oberdiek, texlive-latex-tools, texlive-latex-l3kernel, texlive-latex-l3packages, texlive-latex-fontspec, texlive-latex-amsmath, texlive-latex-amscls, texlive-latex-babel, texlive-latex-cyrillic, texlive-latex-eqparbox, texlive-latex-ifplatform, texlive-latex-etoolbox, texlive-latex-galois, texlive-latex-polyglossia, texlive-tex-texinfo, texlive-latex-changebar, texlive-latex-fancyhdr, texlive-latex-overpic, texlive-latex-parskip, texlive-metapost, texlive-latex-ucs, texlive-generic-pdftex, texlive-latex-media9, texlive-latex-ocgx2, texlive-latex-koma-script, texlive-generic-listofitems, texlive-bibtex, texlive-context-base): Update hashes. (texlive-latex-fontspec)[arguments]: Remove custom build target. (texlive-latex-dinbrief)[arguments]: Add build phase "fix-encoding-error". (texlive-latex-xkeyval): New variable. (texlive-latex-pstool)[source]: Fetch from new location. [build-system]: Use trivial-build-system. [arguments]: Write simple builder. [propagated-inputs]: Add texlive-latex-l3kernel, texlive-latex-tools, and texlive-latex-xkeyval. [synopsis]: Fix typo.
* gnu: irssi: Update to 1.1.2 [fixes CVE-2019-5882].Kei Kebreau2019-01-10
| | | | * gnu/packages/irc.scm (irssi): Update to 1.1.2.
* gnu: docker: Booby-trap "Command" and "LookPath" calls.Danny Milosavljevic2019-01-10
| | | | | * gnu/packages/docker.scm (docker)[arguments]<#:phases>[patch-paths]: Booby-trap "Command" and "LookPath" calls.
* gnu: opendht: Update to 1.8.1.Pierre Neidhardt2019-01-10
| | | | | | | * gnu/packages/crypto.scm (opendht): Update to 1.8.1. [source]: Remove snippet that deletes argon2, which is no longer bundled. [arguments]: Add "--with-argon2" to use system argon2. [license]: Update to GPLv3+ following the README and source headers.
* gnu: Add libsecp256k1.Pierre Neidhardt2019-01-10
| | | | * gnu/packages/crypto.scm (libsecp256k1): New variable.
* gnu: crypto++: Update to 8.0.0.Pierre Neidhardt2019-01-10
| | | | | | * gnu/packages/crypto.scm (crypto++): Update to 8.0.0. [arguments]: Build shared library. [arguments]: Generate .pc file.
* services: docker: Use more minimal service requrements.Danny Milosavljevic2019-01-10
| | | | | | | * gnu/services/docker.scm (docker-service-type)[requirement]: Add file-system-/sys/fs/cgroup/blkio, file-system-/sys/fs/cgroup/cpu, file-system-/sys/fs/cgroup/cpuset, file-system-/sys/fs/cgroup/devices, file-system-/sys/fs/cgroup/memory. Remove elogind.
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